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Phylodynamic Model Adequacy Using Posterior Predictive Simulations.
Journal article

Phylodynamic Model Adequacy Using Posterior Predictive Simulations.

  • Duchene S Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Australia.
  • Bouckaert R Centre for Computational Evolution, University of Auckland, Auckland, New Zealand.
  • Duchene DA School of Life and Environmental Sciences, University of Sydney, Sydney, Australia.
  • Stadler T Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
  • Drummond AJ Centre for Computational Evolution, University of Auckland, Auckland, New Zealand.
  • 2018-06-27
Published in:
  • Systematic biology. - 2019
Computer Simulation
Ebolavirus
Genome, Viral
Hemorrhagic Fever, Ebola
Humans
Influenza A Virus, H1N1 Subtype
Influenza, Human
Phylogeny
Software
English Rapidly evolving pathogens, such as viruses and bacteria, accumulate genetic change at a similar timescale over which their epidemiological processes occur, such that, it is possible to make inferences about their infectious spread using phylogenetic time-trees. For this purpose it is necessary to choose a phylodynamic model. However, the resulting inferences are contingent on whether the model adequately describes key features of the data. Model adequacy methods allow formal rejection of a model if it cannot generate the main features of the data. We present TreeModelAdequacy, a package for the popular BEAST2 software that allows assessing the adequacy of phylodynamic models. We illustrate its utility by analyzing phylogenetic trees from two viral outbreaks of Ebola and H1N1 influenza. The main features of the Ebola data were adequately described by the coalescent exponential-growth model, whereas the H1N1 influenza data were best described by the birth-death susceptible-infected-recovered model.
Language
  • English
Open access status
hybrid
Identifiers
Persistent URL
https://sonar.ch/global/documents/187979
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